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Construction of a high-density genetic map and QTLs mapping for sugars and acids in grape berries.

BMC plant biology (2015-02-04)
Jie Chen, Nian Wang, Lin-Chuan Fang, Zhen-Chang Liang, Shao-Hua Li, Ben-Hong Wu
ABSTRACT

QTLs controlling individual sugars and acids (fructose, glucose, malic acid and tartaric acid) in grape berries have not yet been identified. The present study aimed to construct a high-density, high-quality genetic map of a winemaking grape cross with a complex parentage (V. vinifera × V. amurensis) × ((V. labrusca × V. riparia) × V. vinifera), using next-generation restriction site-associated DNA sequencing, and then to identify loci related to phenotypic variability over three years. In total, 1 826 SNP-based markers were developed. Of these, 621 markers were assembled into 19 linkage groups (LGs) for the maternal map, 696 for the paternal map, and 1 254 for the integrated map. Markers showed good linear agreement on most chromosomes between our genetic maps and the previously published V. vinifera reference sequence. However marker order was different in some chromosome regions, indicating both conservation and variation within the genome. Despite the identification of a range of QTLs controlling the traits of interest, these QTLs explained a relatively small percentage of the observed phenotypic variance. Although they exhibited a large degree of instability from year to year, QTLs were identified for all traits but tartaric acid and titratable acidity in the three years of the study; however only the QTLs for malic acid and β ratio (tartaric acid-to-malic acid ratio) were stable in two years. QTLs related to sugars were located within ten LGs (01, 02, 03, 04, 07, 09, 11, 14, 17, 18), and those related to acids within three LGs (06, 13, 18). Overlapping QTLs in LG14 were observed for fructose, glucose and total sugar. Malic acid, total acid and β ratio each had several QTLs in LG18, and malic acid also had a QTL in LG06. A set of 10 genes underlying these QTLs may be involved in determining the malic acid content of berries. The genetic map constructed in this study is potentially a high-density, high-quality map, which could be used for QTL detection, genome comparison, and sequence assembly. It may also serve to broaden our understanding of the grape genome.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
D-(−)-Fructose, ≥99%
Supelco
Fructose, Pharmaceutical Secondary Standard; Certified Reference Material
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Nitrogen, ≥99.998%
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DL-Malic acid, ReagentPlus®, ≥99%
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D-(−)-Fructose, BioReagent, suitable for cell culture, suitable for insect cell culture
Supelco
D-(−)-Fructose, analytical standard, analytical standard for fructose assay kit, for use with enzymatic assay kit FA20
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D-(−)-Fructose, BioUltra, ≥99.0% (HPLC)
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Tartaric Acid, Pharmaceutical Secondary Standard; Certified Reference Material
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DL-Malic acid, ≥98% (capillary GC)
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Malic acid, Pharmaceutical Secondary Standard; Certified Reference Material
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D-(−)-Fructose, BioXtra
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DL-Malic acid, 99%
USP
Fructose, United States Pharmacopeia (USP) Reference Standard
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Malic acid, meets USP/NF testing specifications
Supelco
DL-Malic acid, analytical standard
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D-(−)-Fructose, meets USP testing specifications
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D-(−)-Fructose, tested according to Ph. Eur.
Millipore
D-(−)-Fructose, suitable for microbiology, ≥99.0%
Fructose, European Pharmacopoeia (EP) Reference Standard
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DL-Malic acid, meets analytical specification of FCC, E296, 99-100.5% (alkalimetric)
USP
Malic acid, United States Pharmacopeia (USP) Reference Standard

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